Jungfraujoch/docs/RUGNUX_INTEGRATION.md

rugnux with other programs

What the reflection files promise to a reading program, and the minimum commands that get each downstream suite running on rugnux output.

:local:
:depth: 2

Reflection-file conventions

mmCIF. Standard items carry their standard meanings — _refln.intensity_meas / _intensity_sigma, the pdbx_I_plus/pdbx_I_minus and pdbx_F_plus/pdbx_F_minus anomalous pairs, _reflns.* and _reflns_shell.* for the merging statistics, _reflns.B_iso_Wilson_estimate for the Wilson B, and _cell.* / _diffrn_radiation_wavelength.wavelength for the geometry.

Anything rugnux reports that has no standard item is written under a jfjoch_ prefix, inside the standard category it belongs to. That is a deliberate choice: a reader that does not know these items ignores them, and one that does can find them without guessing.

item	meaning
_reflns.jfjoch_diffrn_ISa	Asymptotic I/σ in XDS's sense: the whole-range 1/√(a·b) of the error model, so it can be read directly against a CORRECT.LP
_reflns.jfjoch_diffrn_ISa_asymptotic	The strong-reflection tier — the counting-subtracted scatter of well-measured groups. XDS has no equivalent, and it can only ever be the more optimistic of the two. Rotation path only
_reflns.jfjoch_error_model_a, _b	The error model in XDS's convention, σ² = a(σ₀² + b·I²), so the ISa above is re-derivable from the file rather than taken on trust
_reflns.jfjoch_second_moment_I	Twinning second moment ⟨I²⟩/⟨I⟩² — 2.00 untwinned, 1.50 for a perfect twin
_reflns.jfjoch_L_test_mean_abs_L, _L_test_mean_L_squared	Padilla–Yeates L-test. ⟨|L|⟩ is 0.500 untwinned / 0.375 for a perfect twin; ⟨L²⟩ is 0.333 / 0.200. Written only when the test found pairs
_reflns.jfjoch_radiation_damage_relative_B	Relative B from the first to the last rotation batch (Ų); positive is the usual direction, high-resolution intensity fading with dose
_jfjoch_radiation_damage_batch.*	Per-batch loop: id, rotation_start_deg, relative_B
_diffrn_detector.jfjoch_distance_mm, _jfjoch_beam_center_x_pxl, _jfjoch_beam_center_y_pxl	The refined detector geometry actually used, which is not otherwise recoverable from the reflection file
_reflns.pdbx_aniso_B_tensor_eigenvalue_1..3, _pdbx_aniso_B_tensor_eigenvector_*	The anisotropy tensor, eigen-decomposed. Eigenvalues are relative to the weakest direction (so the third is 0 and the first is the anisotropic ΔB), because only the deviatoric part is determined; eigenvectors are in the PDB orthogonalisation convention. Not written for a cubic Laue class, where symmetry forces ΔB to be zero
_reflns.jfjoch_aniso_delta_B, _jfjoch_aniso_delta_B_linear	The anisotropic ΔB, and the part of it that actually follows exp(−½ sᵀBs). The second is what the verdict is gated on
_reflns.jfjoch_aniso_d_min_1..3	Diffraction limit (Å) along each principal direction. A comment marks a value that is the edge of the measured data rather than the crystal's own limit
_reflns.jfjoch_aniso_shape, _jfjoch_aniso_floor, _jfjoch_aniso_significance, _jfjoch_aniso_verdict	The resolution signature of the deficit, the data set's own systematic-error floor, ΔBlinear over that floor, and the resulting verdict. Each carries its vocabulary as a comment

Compatibility note. Before rc.161, _reflns.jfjoch_diffrn_ISa carried the asymptote, not the whole-range value. There is no version marker inside the file, so a number taken from an older .cif is not comparable with one taken from a newer one.

SHELX HKLF 4 (<prefix>.hkl). Fixed-format 3I4,2F8.2 — h k l I σ(I), one record per reflection, terminated by a 0 0 0 record — which is what SHELXC, SHELXD and ANODE expect. Two properties worth knowing before using it:

• Bijvoet mates are written separately, I(+) at +hkl and I(-) at -hkl, so the anomalous differences survive into SHELXC; a reflection with no anomalous split is written once, as its mean.
• Intensities are rescaled by a single global factor so the largest value fits the F8.2 field. I and σ(I) share that factor, so every ratio — and therefore the anomalous signal — is untouched, but the absolute scale is not meaningful. This matters only if you intend to compare magnitudes with another file; SHELXC and ANODE use ratios alone.

MTZ (<prefix>.mtz, and <prefix>_P1.mtz beside it). The CCP4 anomalous layout, with the column types CCP4 programs dispatch on:

H K L IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-) F SIGF F(+) SIGF(+) F(-) SIGF(-) FreeR_flag
H H H    J        Q    K       M    K       M  F    Q    G       L    G       L          I

F is the French–Wilson amplitude. The header carries the determined space group, the refined cell and the wavelength, on a dataset of its own behind the reserved HKL_base, which is where the MTZ format puts them. Older rugnux wrote the data on dataset 0, the id reserved for HKL_base, and CCP4's mtzinfo then reported its 1.54187 Å (Cu Kα) default instead of the real wavelength — every other reader tried, mtzdmp, truncate, ctruncate, gemmi, iotbx and phenix.xtriage, recovered the true value from those files as well, so the effect was confined to that one report. Note that <prefix>_unmerged.mtz still reads 1.54187 under mtzinfo and is not wrong: its columns sit on HKL_base deliberately, as POINTLESS expects, and the wavelength AIMLESS and POINTLESS read is the per-batch one, which is correct. The Bijvoet columns are present on any rotation merge, with or without -A; a stills merge has no Bijvoet split and the file then stops after F SIGF FreeR_flag.

There is deliberately no DANO/SIGDANO pair, the anomalous difference columns a CCP4 merged file usually carries. They are a restatement rather than a measurement: checked column against column on a ctruncate file, DANO is F(+) − F(-) to the last bit and SIGDANO is √(σ(+)² + σ(−)²) to the last bit, on every reflection — the quadrature sum is the convention whether or not the two mates came from one scale model, and no correlation correction is applied by anybody. Every program in the phasing routes below reads the Bijvoet columns directly and forms the difference itself, and CCP4's own phasing engines prefer them: bp3 and afro want F+/SF+/F-/SF- and tell a user holding F/DANO to convert to that form, and mtz2sca ranks I(+/-) over F(+/-) over F/DANO. Where the pair is genuinely wanted — fft's anomalous-difference Fourier takes a DANO label and has no other spelling — one command makes it, with the ISYM column that belongs beside it:

ctruncate -hklin myrun.mtz -hklout myrun_ct.mtz \
    -colin '/*/*/[IMEAN,SIGIMEAN]' -colano '/*/*/[I(+),SIGI(+),I(-),SIGI(-)]'

The unmerged export

<prefix>_unmerged.mtz holds every integrated observation, before scaling and merging, in the column layout POINTLESS writes and aimless, pointless, careless and iotbx.merging_statistics read. It is written by default, in --mode mx and --mode scale alike and with --no-merge as well, and it replaces nothing — rugnux still writes its own merged files in the same run. It needs an output prefix (-o). It is the largest file a run produces, larger on a dense rotation dataset than the merged .mtz, .cif and .hkl put together, so a run that only wants the merged numbers — a regression battery, or a throughput pipeline — turns it off with --no-export-unmerged.

Use it to scale the data with a different program, to have pointless give an independent opinion on the space group, or to compare rugnux's merge against another one on identical input. Each sweep's file is self-contained, so several of them can be handed to pointless and aimless as separate HKLINs to merge sweeps rugnux does not combine itself.

Trap when combining a wild-carded series. For an HKLIN given with wild-cards, POINTLESS accepts the files in order and terminates acceptance at the first file out of chronological order, then merges what it kept and prints a plausible result. Its own keyword lifts the check — ALLOW OUTOFSEQUENCEFILES — or name each file as its own HKLIN, which is not a series; either way, check the file count in its log against the number you meant to give.

Columns. H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP FLAG — POINTLESS's own set — plus four rugnux extras, DELPHI (offset from the centre of the rocking curve), ZETA (the Lorentz geometry of that curve), BGMEAN and BGVAR (the background that was subtracted, and its variance). BATCH is the image ordinal plus one, and a batch header is written for every batch that carries an observation. M/ISYM records both the symmetry operation and the Friedel hand, so the index as measured is recoverable from the index as stored.

Header symmetry and order. The file's MTZ header carries the space group the run determined (P1 where none was), and the rows are sorted on H K L M/ISYM BATCH — the order POINTLESS leaves an unmerged file in, and the order AIMLESS requires of its input — so both programs take the file directly.

What has been applied to the intensities, and what has not. I and SIGI carry the Lorentz-polarization factor and nothing else; the factor itself is in the LP column, so raw counts are I/LP. LP is applied because it is per-observation geometry that varies by more than two orders of magnitude across a sweep and no reader can reconstruct it. Deliberately not applied: the partiality is not divided out (it is reported in FRACTIONCALC), and the per-image scale is not applied at all — those programs fit their own scale model, and handing them pre-scaled data would have them fit a correction to a correction. No resolution cut, outlier rejection or ice-ring filtering is applied either.

Partials. On a rotation run the partials of each reflection are summed into one full, using the same rule rugnux's own 3D combine uses — consecutive frames no more than two apart — and the full is written at the batch its rocking curve is centred on, with the summed rocking-curve fraction in FRACTIONCALC. An event that caught less of its rocking curve than --min-partiality is not written, exactly as in the merge. Summing is the default because a downstream program's own partial handling is far more conservative than rugnux's: given raw partials, aimless accepted a small fraction of the file and merged at a fraction of the multiplicity; given summed fulls it uses essentially all of it. --export-unmerged-partials writes the unsummed form to <prefix>_unmerged_partials.mtz for a program that would rather sum them itself. Stills have no rocking events and are the same either way.

Systematic absences. Lattice-centring absences are not written; screw and glide absences are. Prediction runs in a primitive setting so that the space-group search can test the centring, but the interstitial reflections that leaves make a reading program take the lattice for primitive and demote the group. Screw and glide absences are kept because they are the evidence the space group was chosen on — deleting them would turn a reading program's test into an assumption. XDS and DIALS draw the line in the same place.

Scan axis. The batch headers carry the goniometer axis negated relative to the one in the input file. This is not a correction to the file: rugnux brings an observation made at angle φ back to zero by rotating it by +φ, so the crystal itself turns by −φ, and an MTZ batch header records the axis a batch's own increasing PHI turns the crystal about. With the sign as exported, pointless's independently determined orientation matrix agrees with rugnux's to well under a degree.

Taking the data onward

The reflection files are inputs to other suites, and the handover has a few conventions worth one line each. These are the minimum commands that get each program running on rugnux output.

phenix. The merged files carry both the mean intensity and the Bijvoet pairs, and a phenix program that has not said which it wants stops on the pair of them — from the MTZ and from the mmCIF alike, each listing its own format's labels:

Sorry: Multiple equally suitable arrays of observed xray data found.

Possible choices:
  myrun.mtz:IMEAN,SIGIMEAN
  myrun.mtz:I(+),SIGI(+),I(-),SIGI(-)

Two things are worth knowing before reading that as a fault in the file. The tie is between the two intensity arrays and nothing else: iotbx scores F/SIGF and F(+)/F(-) below them, so they are never in the running and writing amplitudes as well as intensities is not what causes this. And ctruncate's own output ties in the same place — put any merged data through CCP4's truncate step and phenix asks the same question of the result, because a mean intensity array and an anomalous one score equally whenever the calling program has expressed no preference. The only file change that removes the tie is dropping one of the two, and dropping the Bijvoet columns would take the anomalous signal — and the whole SHELX route — with it.

So the answer is a label. The parameter name differs by program, which is the part that catches people out:

phenix.xtriage myrun.mtz xray_data.obs_labels=IMEAN
phenix.xtriage myrun.mtz "xray_data.obs_labels=I(+)"        # the Bijvoet array instead
phenix.refine  model.pdb myrun.mtz miller_array.labels.name=IMEAN

IMEAN on its own is enough — the match is on a substring — and IMEAN,SIGIMEAN and the fully-qualified scaling.input.xray_data.obs_labels= work equally. Quote the anomalous one: the parentheses are shell syntax otherwise. The same behaviour appears on the mmCIF in that format's own vocabulary, and a label from one format does not work on the other (Sorry: No matching array):

phenix.xtriage myrun.cif xray_data.obs_labels=intensity_meas
phenix.xtriage myrun.cif xray_data.obs_labels=pdbx_I_plus

A program that states a preference needs none of this. phenix.hyss, phenix.find_peaks_holes, phenix.molprobity and the data import behind phenix.autosol ask for anomalous data by preference, which breaks the tie for them. phenix.hyss myrun.mtz n_sites=6 scattering_type=S opens the file with no labels given, reports Miller array info: myrun.mtz:I(+),SIGI(+),I(-),SIGI(-), and forms the anomalous differences itself.

The R-free convention. FreeR_flag is 0 = work, 1 = free (the phenix/CNS convention; 5 % free by default). phenix.refine detects that on its own. REFMAC5 does not: its default takes flag 0 as the free set and stops with Error ==> Cannot switch free R flag — give it the keyword FREE 1:

refmac5 XYZIN model.pdb HKLIN myrun.mtz XYZOUT refined.pdb HKLOUT refined.mtz <<eof
LABIN FP=F SIGFP=SIGF FREE=FreeR_flag
FREE 1
NCYC 10
END
eof

POINTLESS / AIMLESS. myrun_unmerged.mtz opens in both directly — it is sorted the way AIMLESS requires and its header carries the determined space group (see The unmerged export). Running pointless first remains the safe route, and its independent space-group opinion is what the file exists for:

pointless HKLIN myrun_unmerged.mtz HKLOUT sorted.mtz
aimless   HKLIN sorted.mtz         HKLOUT scaled.mtz

Several sweeps of one crystal form go in as separate HKLINs to the same pointless run — that is how sweeps rugnux does not combine itself are merged.

careless wants exactly what the unmerged export is — unmerged, unscaled, LP-only intensities with the partiality reported and not divided out. Against its published examples, two renames: BG/SIGBG are called BGMEAN/BGVAR here and BGVAR is a variance, not a sigma; there is no QE column. Hobs/Kobs/Lobs are reconstructed from M/ISYM by reciprocalspaceship, and dHKL careless computes from the cell, so the metadata string that names this file's columns is

careless mono --anomalous "BATCH,dHKL,Hobs,Kobs,Lobs,XDET,YDET,BGMEAN,BGVAR,LP,FRACTIONCALC" \
    myrun_unmerged.mtz out/myrun

Molecular replacement and experimental phasing each get a section of their own below — Phaser and SHELXC/D/E. Both are where rugnux stops and the next program starts, and both meet the one thing the merged intensities could not decide: which of several space groups the data are in.

iotbx.merging_statistics myrun_unmerged.mtz needs no arguments or label choices at all.

Molecular replacement with Phaser

rugnux does not do molecular replacement, so Phaser is the next program for anyone who has a search model. Both CCP4 and phenix ship it — phaser and phenix.phaser, the same 2.8.3 build in the versions this was checked against — and either takes the merged myrun.mtz as it is written.

No LABIN, no label choices. Phaser reads the cell, the space group and the resolution range out of the file and picks the intensity columns itself. Where phenix stops on a merged file because it cannot choose between two equally usable observation arrays (see above), Phaser simply announces what it took:

   Data read from mtz file: myrun.mtz
   Space-Group Name (Hall Symbol): P 41 21 2 ( P 4abw 2nw)
   Unit Cell:   78.06   78.06   37.70   90.00   90.00   90.00
   Column Labels Selected: IMEAN SIGIMEAN
   Resolution on Mtz file:  0.99 39.03

So the whole run is the model and the cell contents:

phaser <<eof
MODE MR_AUTO
HKLIN myrun.mtz
ENSEMBLE model PDBFILE model.pdb IDENTITY 1.0
COMPOSITION PROTEIN MW 14300 NUMBER 1
SEARCH ENSEMBLE model NUMBER 1
ROOT myrun_mr
eof

On a 1.0 Å dataset in a tetragonal point group that run placed one copy at TFZ 11.1, refining to TFZ== 80.3 and LLG 10247, in 54 s of wall clock, with no warnings about the file. The one trap in that script has nothing to do with rugnux: COMPOSITION PROTEIN SEQUENCE wants a file name, and given a chain identifier instead it fails with FILE OPENING ERROR: X before it reads anything. Use MW unless you have the sequence file to hand.

The space group is the interesting part. SPACE_GROUP_NAME in the results report is a scalar and reads like a determination, but it is one of the groups the absences allow, chosen by convention — section 4 says which others it could not separate, as SPACE_GROUP_ALTERNATIVES, and whether the hand is open, as SPACE_GROUP_ENANTIOMORPH= UNDETERMINED. Merged intensities never name a hand: an enantiomorphic pair has the same absences and the same Laue class. Phaser is one of the few programs that can settle it, because a wrong hand simply fails to place the model.

It does this without being asked. MODE MR_AUTO defaults to SGALTERNATIVE SELECT HAND, so the run above listed

   Space Group(s) to be tested:
     P 43 21 2
     P 41 21 2

and returned a single solution in P 43 21 2 — the hand opposite the one in the MTZ header. Nothing in the command asked for that. The space group of the solution is the answer, whichever hand the file happened to carry, and it is on the SOLU SPAC line of the .sol file and in the CRYST1 of the placed model.

When the alternative is not the hand, name it. SPACE_GROUP_ALTERNATIVES also carries screw variants that share a point group — I 2 3 and I 21 3 on a body-centred cubic lattice is the common one — and SGALTERNATIVE SELECT ALL searches every group Phaser derives from the input one by translation symmetry. On a P 41 21 2 input that is all eight of P 4 2 2 … P 43 21 2, and it took the run above from 54 s to 65 s; on an I 2 3 input it is I 2 3, I 21 3 and an origin-shifted I 2 3. To see the list a given file would produce without searching it, MODE CCA prints it and stops:

phaser <<eof
MODE CCA
HKLIN myrun.mtz
COMPOSITION PROTEIN MW 14300 NUMBER 1
ROOT myrun_cca
eof

What Phaser cannot repair from this file is a wrong point group. SGALTERNATIVE moves within one, so a run whose report carries a non-NONE SPACE_GROUP_REFUSED_POINT_GROUP, or a point group you suspect is too high, has to be merged again rather than searched again — myrun_P1.mtz is written for exactly that, and myrun_unmerged.mtz will do it through pointless.

mmCIF is not a route into Phaser. HKLIN myrun.cif stops at FILE OPENING ERROR: myrun.cif, in both the CCP4 and the phenix build — 2.8.3 reads MTZ only. Convert rather than look for a keyword:

gemmi cif2mtz myrun.cif fromcif.mtz

That file gives the same solution — same space group, same placement to a hundredth of a degree, LLG 10248 against 10247. Its amplitude columns come out as FP/SIGFP where rugnux's own MTZ writes F/SIGF, which matters only if you were naming columns by hand; the automatic choice is IMEAN/SIGIMEAN either way. Since rugnux writes the MTZ and the mmCIF in the same run, the conversion is only worth knowing about for a file that arrived without its .mtz.

Experimental phasing with SHELX

shelxc, shelxd and shelxe come with CCP4 (phenix does not ship them). The input is myrun.hkl, and it is the only one of the three reflection files that works: SHELXC 2016/1 reads XDS and SHELX formats, not MTZ, and SAD myrun.mtz gets ** Cannot open file myrun.mtz ** — after which SHELXC exits 0 and writes nothing, so a script has to check for the _fa.hkl it should have produced rather than trust the exit status.

Nothing has to be switched on to get the anomalous signal. A default rotation merge keeps the Bijvoet split, whether or not -A was given: myrun.mtz carries I(+)/I(-) and F(+)/F(-) beside the means, and myrun.hkl writes each mate as its own record, I(+) at +hkl and I(-) at -hkl. -A changes what the merging statistics are counted over, not whether the signal is in the file. The one case with no anomalous columns at all is a stills run, which computes no Bijvoet split; there myrun.hkl holds means only and there is nothing for SHELXC to work with. Unmerged data are not wanted anywhere in this chain either, so a run with --no-export-unmerged is not missing a file SHELX needs.

HKLF 4 carries no metadata, so the cell and the space group have to be repeated on the SHELXC command — take them from UNIT_CELL_CONSTANTS and SPACE_GROUP_NAME in sections 3 and 4 of the report, with the spaces taken out of the group's name. (SHELXC also puts a wavelength in the CELL line of the .ins files it writes; that is its own 0.98 Å default, not anything read from the data, and neither SHELXD nor SHELXE uses it.) The whole chain, for a sulfur substructure — the cell and group here are tetragonal lysozyme's, so substitute your own report's:

shelxc sad <<eof
SAD myrun.hkl
CELL 79.0 79.0 38.0 90 90 90
SPAG P41212
FIND 10
SFAC S
MAXM 2
eof
shelxd sad_fa

SHELXC's own table is the first honest look at whether this is worth continuing — <d"/σ> should be about 0.80 where there is no anomalous signal. Two sweeps are quoted below, both collected at 5 keV for the sulfur signal: a cubic one that went all the way, and a tetragonal one that did not. The cubic one, 2.5 Å at 95 % completeness and multiplicity 30, reads:

 Resl.   Inf. 13.02  8.01  6.03  4.93  4.22  3.71  3.33  3.04  2.80  2.60  2.43
 <I/sig>   108.8  91.4  63.0  64.7  70.6  61.8  45.5  34.7  23.7  12.4   5.0
 %Complete  96.2 100.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0  99.0  72.7
 <d"/sig>   2.58  5.06  3.97  2.92  2.36  1.68  1.50  1.33  1.48  1.38  1.79

SHELXD will separate space groups the merged intensities could not. That sweep's report named a body-centred cubic pair as indistinguishable, so SHELXC and SHELXD were run once per candidate — same reflections, same FIND, only SPAG different. One gave CC 37.93 / CC(weak) 14.05 / CFOM 51.98 and the other CC 46.76 / CC(weak) 22.61 / CFOM 69.37. The substructure is where the screw axis shows itself, and the second group is the right one. This is the same handover as Phaser's arrived at from the other side, and it is worth doing whenever SPACE_GROUP_ALTERNATIVES is not NONE — SHELXD takes seconds, and the pair of runs costs less than reprocessing anything.

SHELXE decides the hand, and says so. Run it twice, -i inverting the substructure. -s is the solvent fraction, -h says the substructure atoms belong to the native structure, as sulfur does, and -a turns on autotracing, which is what actually makes the two hands separate. The two runs write sad.pdb and sad_i.pdb, so they can share a directory:

shelxe sad sad_fa -h -s0.62 -m20 -a15 -q
shelxe sad sad_fa -h -s0.62 -m20 -a15 -q -i

At 63 % solvent the two hands came out at 42.93 % and 15.28 % for the autotrace CC against the native data — pseudo-free CC 66.49 against 37.12, map contrast 0.87 against 0.44, 215 traced atoms — which is a solved structure, from myrun.hkl and nothing else. Where the group is one of the 22 that come in enantiomorphic pairs, SHELXE makes the group change itself: the inverted run prints ** Space group converted to enantiomorph ** and writes the changed group into the CRYST1 of its traced model, so the answer is readable off the output file the same way it is off Phaser's.

A negative result, for calibration. A tetragonal dataset at the same wavelength with the same kind of substructure, but 87 % complete at multiplicity 20 rather than 95 % at 30, gave a plausible SHELXD CFOM 47.62 and then failed at the hand: 15.33 % against 15.60 % autotrace CC, map contrast 0.33 either way. That is not a discrimination and it is not a solution. Nothing about the file was the limit — the anomalous signal SHELXC measured on it was real, <d"/σ> reaching 4.2 — so the reading is that sulfur phasing wants the completeness and the multiplicity, and a .hkl from a sweep that does not have them will get this far and no further.

Comparing the geometry with XDS

Every run logs the detector geometry a second time in XDS's convention, so it can be read straight across against the IDXREF.LP / CORRECT.LP of an XDS run on the same data:

XDS convention: ORGX= 1091.00 ORGY= 1137.00 DETECTOR_DISTANCE= 75.0000
XDS convention: DIRECTION_OF_DETECTOR_X-AXIS= 1.000000 0.000000 0.000000
XDS convention: DIRECTION_OF_DETECTOR_Y-AXIS= 0.000000 1.000000 0.000000
XDS convention: INCIDENT_BEAM_DIRECTION= 0 0 1 X-RAY_WAVELENGTH= 1.000000 QX= QY= 0.075000
XDS convention: ROTATION_AXIS= -1.000000 0.000000 0.000000

XDS is never given this geometry — the XDS plugin supplies image data only, and XDS refines its own from XDS.INP — which is what makes the comparison worth having. The two laboratory frames coincide (x along increasing detector column, y along increasing row, z along the beam), so the numbers are directly comparable, and a tilt appears as the two detector axis vectors rather than as angles, which is how XDS reports it after refinement. Two things to keep in mind: ORGX/ORGY are 1-based, because XDS counts pixels from 1 and Jungfraujoch from 0; and they are the PONI, the same quantity Jungfraujoch's beam centre is — so no correction is needed — but not the direct beam once the detector is tilted (see above).